This invention relates to information storage devices. More particularly, it relates to the use of synthetic DNA polymers for information storage in memory, most particularly secondary optical storage mass memory.
Historically, data processing engines have been physically and conceptually separated from the memory which stores the data and program commands. As processor speed has increased over time, there has been a continuous press for larger memories and faster access. Recent advances in processor speed have caused system bottlenecks in access to memory. This restriction is critical because delays in obtaining instructions or data may cause significant processor wait time, resulting in loss of valuable processing time.
Various approaches have been taken to solve these concerns. Generally, the solutions include using various types of memory which have different attributes. For example, it is common to use a relatively small amount of fast, and typically expensive, memory directly associated with the processor units, typically called cache memory. Additionally, larger capacity, but generally slower, memory such as DRAM or SRAM is associated with the CPU. This intermediate memory is often large enough for a small number of current applications, but not large enough to hold all system programs and data. Mass storage memory, which is ordinary very large, but relatively inexpensive, is relatively slow. While advances have been continually made in improving the size and speed of all types of memory, and generally reducing the cost per bit of memory, there remains a substantial need especially to serve yet faster processors.
For the last 20 years most mass storage devices have utilized a rotating memory medium. Magnetic media have been used for both xe2x80x9cfloppyxe2x80x9d (flexible) disks or xe2x80x9chardxe2x80x9d disk drives. Information is stored by the presence or absence of magnetization at defined physical locations on the disk. Ordinarily, magnetic media are xe2x80x9cread-writexe2x80x9d memories in that the memory may be both written to and read from by the system. Data is written to or read from the disk by heads placed close to the surface of the disk.
A more recent development in rotating mass storage media are the optical media. Compact disks are read only memory in which the presence or absence of physical deformations in the disk indicates the data. The information is read by use of a focused laser beam, in which the change in reflectance properties from the disk indicate the data states. Also in the optical realm are various optical memories which utilize magneto optic properties in the writing and reading of data. These disks are both read only, write once read many (xe2x80x9cWORMxe2x80x9d) drives and multiple read-write memories. Generally, optical media have proved to have a larger storage capacity, but higher costs per bit and limited write ability, as compared with magnetic media.
Several proposals have been made for using polymers for electronic based molecular memories. For example, Hopfield, J. J., Onuchic, J. N. and Beratan, D. N., xe2x80x9cA Molecular Shift Registerxe2x80x9d, Science, 241, p. 817, 1988, discloses a polymer based shift register memory which incorporates charge transfer groups. Other workers have proposed an electronic based DNA memory (see Robinson et al, xe2x80x9cThe Design of a Biochip: A Self-Assembling Molecular-Scale Memory Devicexe2x80x9d, Protein Engineering, 1:295-300 (1987)). In this case, DNA is used with electron conducting polymers for a molecular memory device. Both concepts for these molecular electronic memories do not provide a viable mechanism for inputting data (write) and for outputting data (read).
Molecular electronic memories have been particularly disappointing in their practical results. While proposals have been made, and minimal existence proofs performed, generally these systems have not been converted to commercial reality. Further, a specific deficiency of the system described above is that a sequential memory is typically substantially slower than a random access memory for use in most systems.
The optical memories described above suffer from the particular problem of requiring use of optical systems which are diffraction limited. This imposes size restrictions upon the minimum size of a data bit, thereby limiting memory density. This is an inherent limit in systems which store a single bit of data at a given physical memory location.
Further, in all optical memory systems described above, the information is stored on a bit-by-bit basis, such that only a single bit of data is obtained by accessing a giving physical location in memory. While word-wide memory access systems do exist, generally they store but a single bit of information at a given location, thereby requiring substantially the same amount of physical memory space whether accessed in a bit manner or word-wide manner.
While systems have generally increased in speed and storage density, and decreased in cost per bit, there remains a clear gap at present between processor speed and system requirements. See generally, xe2x80x9cNew Memory Architectures to Boost Performancexe2x80x9d, Tom R. Halfhill, Byte, July, 1993, pp 86 and 87. Despite the general desirability of memories which are faster, denser and cheaper per bit, and the specific critical need for mass memory which can meet the demands of modern day processor systems speed, no completely satisfactory solution has been advanced heretofore. The fundamental limitations on the currently existing paradigms cannot be overcome by evolutionary enhancements in those systems. This invention constitutes a new memory paradigm.
Synthetic DNA polymers are used as an optical storage media for memory. In the preferred embodiment, a three-dimensional memory is formed having three spatial dimensions. Multiple bit information is read as different color wavelengths of light emitted through diffraction limited optical portals on the surface of the media.
Structurally, a planar substrate (x-y dimension) has multiple, physically separate read portals or read locations disposed upon its surface. In the preferred embodiment, the substrate is disk shaped and the read portals are arranged in radial tracks or on a decreasing radius spiral around the center of the substrate. The read portal is that area which will be illuminated by a read illumination source to provide output from the memory. The read portal contains within it one or more DNA chromophoric memory units. In the preferred embodiment, each DNA chromophoric memory unit is composed of a DNA template, onto which are attached donor and acceptor units. Functionalized DNA polymers have various arrangements of chromophoric donors, chromophoric acceptors and quenchers. The quenchers are associated with the donor and/or the acceptor. The functionalized DNA polymers containing the donor/acceptor/quencher groups are arranged on the planar surface of the media so as to project into the z-spatial dimension. The chromophoric memory unit is attached to the substrate.
To write to the memory, the response properties of the chromophoric memory unit are changed. In the preferred embodiment, a photochemical reaction destroys or inactivates the quencher. A write source serves as the illumination source for the photochemical reaction. In the preferred embodiment, the quencher may be inactivated by light, most preferably UV light, and is formed with photocleavable linkers, or by derivitization of chromophore molecules with photoactive groups. Thus, the basic memory information is determined by whether the quencher is active or not.
To read from the memory, preferably a single wavelength light is used to illuminate the read portal. A read illumination source illuminates the read portal, including the various chromophoric memory units contained within the portal, providing excitation illumination to the donor units in the chromophoric memory units. If the quencher is not active, the chromophoric memory unit, via the acceptor, radiates to the read detector. However, if the qencher is active, no output occurs. In this way, all chromophoric memory units in a read portal may be simultaneously probed. If multiple chromophoric memory units having various output wavelengths or other detectable parameters are included within a read portal, a multiple bit or word-wide output may be obtained from a diffraction limited read portal.
In the preferred embodiment, the chromophoric memory unit utilizes energy transfer between the donor and acceptor, via the Fxc3x6rster energy transfer mechanism. Fxc3x6rster energy transfer is a non-radiative energy transfer mechanism which utilizes dipole-dipole coupling. The energy transfer mechanism allows a single wavelength of light to excite all acceptor chromophores.
In one embodiment, multiple write wavelengths are used to selectively activate or deactivate separate wavelength sensitive quenchers. If multiple wavelength sensitive quenchers are utilized, the various chromophoric memory units located within a given read portal may have various chromophoric responses. Multiple write wavelengths may then be selectively used to activate or inactivate quenchers. Upon illumination from the read illumination source, those chromophoric memory units whose output is not quenched will provide multiple wavelength output to the read detector. However, those chromophoric memory units whose output is quenched will not provide output.
In another embodiment, the read or optical portal is further spatially subdivided (x-y dimension) into multiple write sublocations. Each write sublocation is written to separately from the other write sublocations in a read portal. In the preferred embodiment, a given write sublocation contains chromophoric memory units whose primary output wavelength is spectrally resolvable as compared to the output from other write sublocations. By writing separately to the individual write sublocations, a single quencher material may be used for multiple read wavelengths.
In another aspect of this invention, the output of the read wavelength from the write sublocation may be varied. In the preferred embodiment, small wavelength shift substrates, various intensity states and/or polarization states may be affected by the use of multiple quenchers activated by different write wavelengths. By way of example, utilizing a read portal of approximately 1 micron2, 16 separate write sublocations may be formed. Utilizing separate chromophoric acceptors for each of the write sublocations results in a 16 bit wide word output from the read portal. Utilizing one of the variations of wavelength shift substrates, intensity states and/or polarization states can directly produce a 64 bit wide word from a single sub-micron sized or diffraction limited read portal.
Accordingly, it is an object of this invention to provide an improved mass storage system.
It is yet a further object of this invention to provide a mass storage system with word-wide data output from a single potentially diffraction limited read location.
It is yet a further object of this invention to increase the planar surface storage density and capacity of memory.
It is an object of this invention to provide a memory having an increased data transfer rate.
It is yet a further object of this invention to provide a nanoscale storage location for memory applications.
It is a object of this invention to utilize functionalized synthetic DNA polymers for non-biological applications.
It is yet a further object of this invention to provide a write once read many (WORM) disk drive.
It is yet a further object of this invention to utilize synthetic DNA polymers as a memory material.
It is yet a further object of this invention to utilize synthetic DNA polymers as a nanofabrication material.